Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg-big/zr3644_2_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fq.gz

Data processed at 23:10:10 on 2021-06-09


Alignment Stats

Sequence pairs analysed in total 100000
Paired-end alignments with a unique best hit 61033
Pairs without alignments under any condition 22427
Pairs that did not map uniquely 16540
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 2176242
Methylated C's in CpG context 28402
Methylated C's in CHG context 1868
Methylated C's in CHH context 7614
Methylated C's in Unknown context 76
Unmethylated C's in CpG context 251780
Unmethylated C's in CHG context 374557
Unmethylated C's in CHH context 1512021
Unmethylated C's in Unknown context 5381
Percentage methylation (CpG context) 10.1%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 15101 original top strand
CTOT 15016 complementary to original top strand
CTOB 15459 complementary to original bottom strand
OB 15457 original bottom strand

Deduplication

Alignments analysed 61033
Unique alignments 56894
Duplicates removed 4139
Duplicated alignments were found at 3852 different positions

Cytosine Methylation after Extraction

Total C's analysed 1418146
Methylated C's in CpG context 18079
Methylated C's in CHG context 1195
Methylated C's in CHH context 4889
Unmethylated C's in CpG context 163292
Unmethylated C's in CHG context 242611
Unmethylated C's in CHH context 988080
Percentage methylation (CpG context) 10.0%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot